Switzerland suggested itinerary

From where are you starting ? Geneva, Basel or Zurich ?

DAY 1 Geneva - Montreux - Interlaken, could take a boat between Spiez and Interlaken (it's included in your pass)

DAY 2 Interlaken area with great hikes but... trains aren't included if going to Grindelwald, Lauterbrunnen, etc. (25% discount)

DAY 3 Interlaken - Lucerne - Rigi : 50% discount on the boat ride between Lucerne and Vitznau to go up or fully included if going via Arth-Goldau (I recommend to do one leg by boat and the other by train : the boat journey is impressive but expensive too)

Night in Lucerne

DAY 4 Lucerne - Göschenen - Andermatt - Disentis/Muster - Reichenau-Tamins (or Chur) - St. Moritz (from Andermatt it is part of the Glacier Express route, except it's on regional trains which are reservation-free)

DAY 5 St. Moritz - Tirano (there are open wagons in summer) and then take the 14:24 Bernina Express (there are reservation-free coaches up front) to Chur and then take the night train from Buchs SG to Zagreb.

That is only one itinerary, you could skip Interlaken and go to Zermatt instead for example.

DAY 1 Basel - Bern - Spiez - boat to Interlaken

DAY 2 Interlaken - Spiez - Historic Lötschberg route - Brig - Zermatt

DAY 3 Zermatt : ride to the Gornergrat with amazing views (but not included...), in the afternoon take a train to Brig and Andermatt (part of the Glacier Express route)

DAY 4 Andermatt - Göschenen - Historic Gotthard route - Bellinzona - Locarno/Lugano

DAY 5 (Locarno -) Lugano - Tirano with a bus along Lake Como. It is included but you need a reservation.

14:23 Bernina Express train (on the reservation-free coaches, with windows that can be opened) to Chur and then night train Buchs SG - Zagreb

Let me know if you've got any places you want to see and I can help you... there are just too many possibilities right now.

Apart from the second half of the 5th day everything is open I'd say.

Thank you. Will be starting from Paris so will maybe head from there to Geneva and ultimately Zurich and perhaps look to base there for 2/3 nights 

Is the Buchs to Zagreb train a sleeper?

Ok that changes everything then. Zurich could be a base but it means long travel days.

DAY 1 Paris - Bellegarde (10€ seat reservation on the TGV) - Geneva in a regional train.

You save a lot of money by changing in Bellegarde and it's no more tan half an hour longer.

Geneva is worth a quick but not much more I'd say.

Train Geneva - Lausanne

DAY 2 Lausanne - Montreux - Interlaken with the Golden Pass panoramic train (there are only a handful direct trains between Montreux-Interlaken but there are hourly trains with a change in Zweisimmen and Spiez)

DAY 3 

Interlaken - Brienz by boat (included)

Brienz - Lucerne - Vitznau (50% discount boat) - Rigi - Arth-Goldau - Zurich

DAY 4 Zurich - Bellinzona - Locarno/Lugano with the 57-km Gotthard Tunnel one-way and the Gotthard Historic route back

DAY 5 07:38 Zurich - Landquart - Sagliains - Pontresina - Tirano 13:00

14:24 Tirano - Chur 18:22 Bernina Express

Sort of a round-trip as you take the Vereina line one-way and the Albula line back

Sleeper train Buchs SG - Zagreb : you need a reservation for the seats, couchettes or sleepers.

Thanks very much for this information. I would prefer shorter travel days so May have to rethink number of nights inn Zurich.  

As Zürich is one of the most expensive cities in the world I would consider having the base somewhere else in Switzerland. Even if the whole of Switzerland is expensive, Zürich is exceptional.